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Forum: Bioinformatics

10-24-2013, 08:00 AM

Replies: 0

How does Tophat balance read-mismatches with seqment-mismatches?

Views: 1,226

Posted By zshuhua

How does Tophat balance read-mismatches with seqment-mismatches?

Hello,
I'm using Tophat v 2.05 to map 75 bases single end reads generated by Illumina Hi-seq2000. I set segment-length with 25 as default and want to maximum mismatches of 3 allowed for each read....

Forum: Introductions

05-10-2013, 07:28 AM

Replies: 3

FastQC: odd kmer content

Views: 2,833

Posted By zshuhua

Thanks for your help! I intend to calculate...

Thanks for your help!
I intend to calculate genes/transcripts expression levels. Do I have to cut the 5' 10 bp?
I'm wondering what causes the patterns of for GGGGG, AAAAA and TCTTC, because I saw...

Forum: Bioinformatics

05-09-2013, 08:44 AM

Replies: 25

Removing primers, adaptors, how to know if it's good?

Views: 6,461

Posted By zshuhua

Hi, So, all the barcodes are NOT included in...

Hi,
So, all the barcodes are NOT included in the read sequences but only in their IDs. We only need to trim adapters but not barcodes.

Forum: Introductions

05-09-2013, 06:53 AM

Replies: 3

FastQC: odd kmer content

Views: 2,833

Posted By zshuhua

FastQC: odd kmer content

Hi,
I'm checking the data quality using fastqc for the Illumina Hi-Seq2000 reads and got odd kmer patterns (see attachment). Although an old thread suggested that 5' pattern is common, I want to...

Showing results 1 to 4 of 4

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